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Shipman, Seth

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Shipman

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Seth

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Shipman, Seth
Author's Publications: search.filters.isAuthorOfPublication.03ca1104-b403-4e53-b3a7-de53b34509d7

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    Rapid neurogenesis through transcriptional activation in human stem cells
    (Blackwell Publishing Ltd, 2014) Busskamp, Volker; Lewis, Nathan E; Guye, Patrick; Ng, Alex HM; Shipman, Seth; Byrne, Susan M; Sanjana, Neville E; Murn, Jernej; Li, Yinqing; Li, Shangzhong; Stadler, Michael; Weiss, Ron; Church, George
    Advances in cellular reprogramming and stem cell differentiation now enable ex vivo studies of human neuronal differentiation. However, it remains challenging to elucidate the underlying regulatory programs because differentiation protocols are laborious and often result in low neuron yields. Here, we overexpressed two Neurogenin transcription factors in human-induced pluripotent stem cells and obtained neurons with bipolar morphology in 4 days, at greater than 90% purity. The high purity enabled mRNA and microRNA expression profiling during neurogenesis, thus revealing the genetic programs involved in the rapid transition from stem cell to neuron. The resulting cells exhibited transcriptional, morphological and functional signatures of differentiated neurons, with greatest transcriptional similarity to prenatal human brain samples. Our analysis revealed a network of key transcription factors and microRNAs that promoted loss of pluripotency and rapid neurogenesis via progenitor states. Perturbations of key transcription factors affected homogeneity and phenotypic properties of the resulting neurons, suggesting that a systems-level view of the molecular biology of differentiation may guide subsequent manipulation of human stem cells to rapidly obtain diverse neuronal types.
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    Molecular recordings by directed CRISPR spacer acquisition
    (American Association for the Advancement of Science (AAAS), 2016) Shipman, Seth; Nivala, Jeffrey; Macklis, Jeffrey; Church, George
    The ability to write a stable record of identified molecular events into a specific genomic locus would enable the examination of long cellular histories and have many applications, ranging from developmental biology to synthetic devices. We show that the type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas system of Escherichia coli can mediate acquisition of defined pieces of synthetic DNA. We harnessed this feature to generate records of specific DNA sequences into a population of bacterial genomes. We then applied directed evolution so as to alter the recognition of a protospacer adjacent motif by the Cas1-Cas2 complex, which enabled recording in two modes simultaneously. We used this system to reveal aspects of spacer acquisition, fundamental to the CRISPR-Cas adaptation process. These results lay the foundations of a multimodal intracellular recording device.
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    CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria
    (2017) Shipman, Seth; Nivala, Jeff; Macklis, Jeffrey; Church, George
    DNA is an excellent medium for data archival. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro1–6. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1-Cas2 integrase, the CRISPR-Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity7. Harnessed, this system has the potential to write arbitrary information into the genome8. Here, we use the CRISPR-Cas system to encode images and a short movie into the genomes of a population of living bacteria. In doing so, we push the technical limits of this information storage system and optimize strategies to minimize those limitations. We additionally uncover underlying principles of the CRISPR-Cas adaptation system, including sequence determinants of spacer acquisition relevant for understanding both the basic biology of bacterial adaptation as well as its technological applications. This work demonstrates that this system can capture and stably store practical amounts of real data within the genomes of populations of living cells.